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comparison commons/core/sql/test/Test_TableMatchAdaptator.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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1 # Copyright INRA (Institut National de la Recherche Agronomique)
2 # http://www.inra.fr
3 # http://urgi.versailles.inra.fr
4 #
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 #
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 #
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 #
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30
31
32 import unittest
33 import time
34 import os
35 from commons.core.sql.DbMySql import DbMySql
36 from commons.core.coord.Match import Match
37 from commons.core.sql.TableMatchAdaptator import TableMatchAdaptator
38
39
40 class Test_TableMatchAdaptator( unittest.TestCase ):
41
42 def setUp( self ):
43 self._uniqId = "%s_%s" % (time.strftime("%Y%m%d%H%M%S") , os.getpid())
44 self._configFileName = "dummyConfigFile_%s" % self._uniqId
45 self._iDb = DbMySql()
46 self._table = "dummyMatchTable_%s" % self._uniqId
47 self._tMatchA = TableMatchAdaptator( self._iDb, self._table )
48
49 def tearDown( self ):
50 self._uniqId = None
51 self._iDb.dropTable( self._table )
52 self._iDb.close()
53 self._table = None
54 self._tMatchA = None
55
56 ##################################################################################
57 ################## Tests for methods in ITableMatchAdaptator #####################
58 ##################################################################################
59 def test_insert(self):
60 match = Match()
61
62 tuple = ("QName1", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
63
64 match.setFromTuple(tuple)
65
66 self._iDb.createTable( self._table, "match", "" )
67 self._tMatchA.insert( match, False )
68
69 expTMatchTuple = (('QName1', 1L, 5L, 5L, 0.1, 0.2, 'SName1', 5L, 25L, 20L, 0.15, 1e-20, 15L, 87.2, 1L),)
70
71 sqlCmd = "SELECT * FROM %s" % ( self._table )
72 self._iDb.execute( sqlCmd )
73 obsTmatchTuple = self._iDb.cursor.fetchall()
74
75 self.assertEquals( expTMatchTuple, obsTmatchTuple )
76
77
78 def test_insert_empty_match(self):
79 match = Match()
80
81 tuple = ("", -1, -1, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
82
83 match.setFromTuple(tuple)
84
85 self._iDb.createTable( self._table, "match", "" )
86 self._tMatchA.insert( match, False )
87
88 expTMatchTuple = ()
89
90 sqlCmd = "SELECT * FROM %s" % ( self._table )
91 self._iDb.execute( sqlCmd )
92 obsTmatchTuple = self._iDb.cursor.fetchall()
93
94 self.assertEquals( expTMatchTuple, obsTmatchTuple )
95
96
97 def test_insertList(self):
98 match1 = Match()
99 match2 = Match()
100
101 tuple1 = ("QName1", 1, 5, 5, 0.1, 0.2, "SName1", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
102 tuple2 = ("QName2", 2, 5, 5, 0.1, 0.2, "SName2", 6, 25, 20, 0.15, 1e-20, 15, 87.2, 2)
103
104 match1.setFromTuple(tuple1)
105 match2.setFromTuple(tuple2)
106
107 self._iDb.createTable( self._table, "match", "" )
108 self._tMatchA.insertList( [ match1, match2 ], False )
109
110 expTMatchTuple = (('QName1', 1L, 5L, 5L, 0.1, 0.2, 'SName1', 5L, 25L, 20L, 0.15, 1e-20, 15L, 87.2, 1L),\
111 ('QName2', 2L, 5L, 5L, 0.1, 0.2, 'SName2', 6L, 25L, 20L, 0.15, 1e-20, 15L, 87.2, 2L))
112
113 sqlCmd = "SELECT * FROM %s" % ( self._table )
114 self._iDb.execute( sqlCmd )
115 obsTmatchTuple = self._iDb.cursor.fetchall()
116
117 self.assertEquals( expTMatchTuple, obsTmatchTuple )
118
119
120 def test_getMatchListFromQuery(self):
121 self._iDb.createTable( self._table, "match", "" )
122 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
123 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
124 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
125 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
126 match1 = Match()
127 match1.setFromTuple( tuple1 )
128 match2 = Match()
129 match2.setFromTuple( tuple2 )
130 match3 = Match()
131 match3.setFromTuple( tuple3 )
132 match4 = Match()
133 match4.setFromTuple( tuple4 )
134 expListMatch = [ match1, match2, match3, match4 ]
135 self._tMatchA.insertList(expListMatch)
136
137 obsListMatch = self._tMatchA.getMatchListFromQuery("QName")
138
139 self.assertEquals(expListMatch, obsListMatch)
140
141
142 def test_getMatchListFromQuery_unexisted_seq_name(self):
143 self._iDb.createTable( self._table, "match", "" )
144 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
145 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
146 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
147 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
148 match1 = Match()
149 match1.setFromTuple( tuple1 )
150 match2 = Match()
151 match2.setFromTuple( tuple2 )
152 match3 = Match()
153 match3.setFromTuple( tuple3 )
154 match4 = Match()
155 match4.setFromTuple( tuple4 )
156 lMatch = [ match1, match2, match3, match4 ]
157 self._tMatchA.insertList(lMatch)
158
159 expListMatch = []
160 obsListMatch = self._tMatchA.getMatchListFromQuery("Dummy")
161
162 self.assertEquals(expListMatch, obsListMatch)
163
164
165 def test_getMatchListFromId(self):
166 self._iDb.createTable( self._table, "match", "" )
167 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
168 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
169 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
170 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
171 match1 = Match()
172 match1.setFromTuple( tuple1 )
173 match2 = Match()
174 match2.setFromTuple( tuple2 )
175 match3 = Match()
176 match3.setFromTuple( tuple3 )
177 match4 = Match()
178 match4.setFromTuple( tuple4 )
179 lMatch = [ match1, match2, match3, match4 ]
180 expListMatch = [ match1 ]
181 self._tMatchA.insertList(lMatch)
182
183 obsListMatch = self._tMatchA.getMatchListFromId(1)
184
185 self.assertEquals(expListMatch, obsListMatch)
186
187
188 def test_getMatchListFromIdList_empty_id_list( self ):
189 self._iDb.createTable( self._table, "match", "" )
190 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
191 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
192 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
193 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
194 match1 = Match()
195 match1.setFromTuple( tuple1 )
196 match2 = Match()
197 match2.setFromTuple( tuple2 )
198 match3 = Match()
199 match3.setFromTuple( tuple3 )
200 match4 = Match()
201 match4.setFromTuple( tuple4 )
202 lMatch = [ match1, match2, match3, match4 ]
203 self._tMatchA.insertList(lMatch)
204
205 expList = []
206 obsList = self._tMatchA.getMatchListFromIdList([])
207 self.assertEquals(expList, obsList)
208
209
210 def test_getMatchListFromIdList( self ):
211 self._iDb.createTable( self._table, "match", "" )
212 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
213 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
214 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
215 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
216 match1 = Match()
217 match1.setFromTuple( tuple1 )
218 match2 = Match()
219 match2.setFromTuple( tuple2 )
220 match3 = Match()
221 match3.setFromTuple( tuple3 )
222 match4 = Match()
223 match4.setFromTuple( tuple4 )
224 lMatch = [ match1, match2, match3, match4 ]
225 self._tMatchA.insertList(lMatch)
226
227 lObs = self._tMatchA.getMatchListFromIdList((1, 2, 3))
228
229 lExp = [match1, match2, match3]
230 self.assertEquals(lExp, lObs)
231
232 def test_getListOfAllMatches( self ):
233 self._iDb.createTable( self._table, "match", "" )
234 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
235 tuple2 = ("QName", 1, 6, 6, 0.2, 0.1, "SName", 6, 26, 10, 0.18, 1e-30, 18, 85.2, 2)
236 tuple3 = ("QName", 1, 7, 8, 0.1, 0.2, "SName", 5, 20, 15, 0.20, 1e-25, 20, 89.0, 3)
237 tuple4 = ("QName", 1, 8, 8, 0.1, 0.1, "SName", 5, 15, 10, 0.17, 1e-23, 14, 89.5, 4)
238 match1 = Match()
239 match1.setFromTuple( tuple1 )
240 match2 = Match()
241 match2.setFromTuple( tuple2 )
242 match3 = Match()
243 match3.setFromTuple( tuple3 )
244 match4 = Match()
245 match4.setFromTuple( tuple4 )
246 lMatch = [ match1, match2, match3, match4 ]
247 expList = [ match1, match2, match3, match4 ]
248 self._tMatchA.insertList(lMatch)
249
250 obsList = self._tMatchA.getListOfAllMatches()
251 self.assertEqual( expList, obsList )
252
253
254 def test_getListOfAllMatches_empty_table( self ):
255 self._iDb.createTable( self._table, "match", "" )
256 expList = []
257 obsList = self._tMatchA.getListOfAllMatches()
258 self.assertEqual( expList, obsList )
259
260
261 test_suite = unittest.TestSuite()
262 test_suite.addTest( unittest.makeSuite( Test_TableMatchAdaptator ) )
263 if __name__ == "__main__":
264 unittest.TextTestRunner(verbosity=2).run( test_suite )